When a High Elf has a Great Weapon does he still get to re-roll misses of "to hit" rolls because of his higher initiative? I understand that they cancel each other out and you strike at your regular initiative, but that mean the model losses their re-rolls too?

Some would argue that the model still has the ASF rule which means that they still get their re-rolls due to the wording of the rule in the book. The rule basically says a model with this special rule may re-roll missed to hit rolls if they have an initiative equal to or higher than their opponent.

This is poor practice though and though the rules aren't definitive normal gameplay is that ASF is cancelled/removed by ASL so the model no longer has that special rule.